Usage example

A standard example of CrystalFp invocation.

cfp \
    --verbose=3 \
    --elements="Si O" \
    --cutoff-distance=30 \
    --fingerprint-method=0 \
    --distance-method=0 \
    --grouping-method=1 \
    --grouping-threshold=0.000002 \
    --remove-dupl=map.dat \
    --checkpoint-dir=./chk \
    --summary=summary.dat \
    --fld-fingerprints=fp.fld  \
    --fld-distances=dist.fld \
    --sorted-distances=sorted.dat \
    gatheredPOSCARS \
    enthalpies_nospace.dat

Verbose: show also the progress of the various computations (on standard error). Compute the fingerprints with a cutoff distance of 30 using the "Per element diffraction" method (number 0). Use distance measure "Cosine distance" (number 0) and grouping method "Hierarchical Single Linkage" (number 1) with a threshold of 2e-6. Based on the grouping, remove duplicates and put the correspondence [new index-old index] in the map.dat file. All the fingerprint details are saved in the ./chk directory that will be reloaded in case of crash or to compute lower dimensionality values (use –force-dim=newDim). The gatheredPOSCARS file contains the structures and the enthalpies_nospace.dat file the corresponding energies.

The above example produces the following files (documentation on the Output file formats page):

• summary.dat with computation summary data
• fp.fld and fp.dat with the fingerprints (the fld file is useful to load the result inside AVS/Express)
• dist.fld and dist.dat with the distancew matrix (the fld file is useful to load the result inside AVS/Express)
• sorted.dat with the sorted distances